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Title: CoBAMP: a Python framework for metabolic pathway analysis in constraint-based models

Abstract

Abstract Summary CoBAMP is a modular framework for the enumeration of pathway analysis concepts, such as elementary flux modes (EFM) and minimal cut sets in genome-scale constraint-based models (CBMs) of metabolism. It currently includes the K-shortest EFM algorithm and facilitates integration with other frameworks involving reading, manipulation and analysis of CBMs. Availability and implementation The software is implemented in Python 3, supported on most operating systems and requires a mixed-integer linear programming optimizer supported by the optlang framework. Source-code is available at https://github.com/BioSystemsUM/cobamp.

Authors:
ORCiD logo [1]; ORCiD logo [1];
  1. Centre of Biological Engineering, University of Minho, Braga 4710-057, Portugal
Publication Date:
Sponsoring Org.:
USDOE Office of Nuclear Energy (NE), Fuel Cycle Technologies (NE-5)
OSTI Identifier:
1563062
Grant/Contract Number:  
UID/BIO/04469/2019; NORTE-01-0145-FEDER-000004; SFRH/BD/118657/2016
Resource Type:
Publisher's Accepted Manuscript
Journal Name:
Bioinformatics
Additional Journal Information:
Journal Name: Bioinformatics; Journal ID: ISSN 1367-4803
Publisher:
Oxford University Press
Country of Publication:
United Kingdom
Language:
English

Citation Formats

Vieira, Vítor, Rocha, Miguel, and Valencia, ed., Alfonso. CoBAMP: a Python framework for metabolic pathway analysis in constraint-based models. United Kingdom: N. p., 2019. Web. doi:10.1093/bioinformatics/btz598.
Vieira, Vítor, Rocha, Miguel, & Valencia, ed., Alfonso. CoBAMP: a Python framework for metabolic pathway analysis in constraint-based models. United Kingdom. doi:10.1093/bioinformatics/btz598.
Vieira, Vítor, Rocha, Miguel, and Valencia, ed., Alfonso. Mon . "CoBAMP: a Python framework for metabolic pathway analysis in constraint-based models". United Kingdom. doi:10.1093/bioinformatics/btz598.
@article{osti_1563062,
title = {CoBAMP: a Python framework for metabolic pathway analysis in constraint-based models},
author = {Vieira, Vítor and Rocha, Miguel and Valencia, ed., Alfonso},
abstractNote = {Abstract Summary CoBAMP is a modular framework for the enumeration of pathway analysis concepts, such as elementary flux modes (EFM) and minimal cut sets in genome-scale constraint-based models (CBMs) of metabolism. It currently includes the K-shortest EFM algorithm and facilitates integration with other frameworks involving reading, manipulation and analysis of CBMs. Availability and implementation The software is implemented in Python 3, supported on most operating systems and requires a mixed-integer linear programming optimizer supported by the optlang framework. Source-code is available at https://github.com/BioSystemsUM/cobamp.},
doi = {10.1093/bioinformatics/btz598},
journal = {Bioinformatics},
number = ,
volume = ,
place = {United Kingdom},
year = {2019},
month = {7}
}

Journal Article:
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This content will become publicly available on July 29, 2020
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